/two_locus_selection

Manuscript repo for two-locus

Primary LanguagePython

Two-locus selection using moments

This repository contains scripts to run the analyses and compile the manuscript for "Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes" (formerly "Can we distinguish modes of selective interactions using linkage disequilibrium?"). The manuscript is built using bookdown, and the repository was first cloned from kevin thornton's very handy rmarkdown manuscript template.

Changelog

Tagged commits correspond to submissions, revisions, etc, with a short description of changes between versions.

0.1

0.2

  • Resubmission with major revisions, April 1, 2022

Required R packages

Manuscript compilation uses bookdown and rmarkdown. At the very least, you need:

  • bookdown
  • rmarkdown
  • knitr

Required Python packages

For analyses:

  • moments >= 1.1.0 (includes scipy and numpy)

For plotting:

  • matplotlib
  • bokeh